NAR Molecular Biology Database Collection entry number 1257
Ding, G.1, Lorenz, P.2, Kreutzer, M.2, Li, Y.1,3, Thiesen, H.-J.2
1Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
2Institute of Immunology, Schillingallee 70, University of Rostock, D-18055 Rostock, Germany
3Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, P. R. China

Database Description

SysZNF provides a systematic catalogue of (until now) human and mouse C2H2 zinc finger genes/proteins based on HMM profile searches of the whole proteomes with the PFAM profile of the C2H2 domain (accession number: PF00096; C2H2 zinc-finger proteins often contain additional conserved domains, such as KRAB, SCAN, BTB, and SET. These effector domains are usually found in the amino-terminal region of the proteins and often serve different roles in transcriptional regulation through their ability to interact with other cellular molecules. A comprehensive database has been developed with a web interface that i) arranges C2H2 gene information based on physical localization in the respective genome, ii) provides downloadable and visual information on gene organization and protein domain composition, iii) serves as starting point to search and examine ortholog and paralog relationships in different species and iv) contains direct links from a particular data set to other resources of the scientific community. In SysZNF, each C2H2-ZNF gene is represented as a card to integrate the related information from public databases. A graphical gene model system, a protein display system and a gene cluster display system were developed for these genes. The database should help in i) quickly gathering information on gene models, protein organization of particular ZNF genes/proteins, ii) providing the user with quick links to other biological databases, iii) suggesting orthologs and paralogs between species, and iv) generally providing basic information and leads for further experimentation. Thus, SysZNF should facilitate the research on C2H2 type ZNF genes under an integrative view in comparative genomic approaches.

Go to the abstract in the NAR 2009 Database Issue.
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